That price sounds about right for the list of things, but you have TONS of unneeded stuff. As mentioned, the only thing necessary for stage 2 is the downpipe.
The intercooler is useful, but not required and requires a bunch of labor to get in (removing front bumper, etc...), and it's better to go with a cheaper intercooler as the more expensive ones are just overpriced. The Unitronic intercooler is a middle ground, and people have had success with even the cheap ebay intercoolers.
The Carbon fiber intake is 100% looks and effectively makes no difference at all to engine performance on the mk7 (the stock airbox is pretty good). I would ditch that entirely as it's also extremely overpriced.
The dogbone mount is a fantastic mod in general, but it's a single bolt so I recommend doing it yourself.
Spark plugs are more of an as needed thing, and are also very easy to do yourself, but they probably aren't a significant cost adder.
Also, that shop is ripping you off big time, even for stage 1, with the APR holiday discount the price of stage 1 + TCU tune is $1100, so the shop is trying to charge you $400 to sit there with a computer for 15 minutes while something loads. They are scummy.
